Metagenome puzzle illustrating the reconstruction of microbial genomes with computer algorithms
After many years of data analysis and modelling behind her computer, Dr Julia Engelmann, Tenure Track Scientist at the Marine Microbiology & Biogeochemistry department, literally and figuratively got her feet wet in 2019! She joined an actual expedition on the RV Navicula. ‘The sea was a bit rough on some days, but it definitely tasted like more.’
Computational biologist Julia Engelmann studies micro-organisms in marine systems, with a focus on the Wadden and the North Sea. ‘To be more precise: I use mathematical models to look for possible relations between organisms. For example, if bacterial species A is always present with another specific species B, one could assume that they have some kind of biological relationship. Maybe one provides a specific substrate for the other? You have to be careful with correlations, though. They might also co-occur because they just prefer the same habitat. With network modelling, I integrate biological abundance data with physicochemical data, to try to disentangle these relationships.’
In 2019, Engelmann went on her first expedition on the RV Navicula, the NIOZ Research Vessel that regularly sails the Wadden and the North Sea. ‘My first sea-going expedition was a light version’, Engelmann admits. ‘We were at sea for only five days.’ Despite relatively rough weather, Engelmann and her expedition leader Dr Helge Niemann were able to sample the Wadden Sea water on an hourly basis for 48 hours. ‘Apart from collecting microorganisms from the water to extract their DNA, we also took samples to determine nutrient concentrations and measured salinity and temperature. All of these will be integrated into the computer models. Currently, we are still in the process of preparing our samples for DNA sequencing. We are using new sequencing technology, and establishing protocols unfortunately takes time. But I am very anxious to see what the hourly variation in microbes will be in relation to, for example, the salinity of the water.’
Ciliate between Spirillum bacteria
Ciliates (Chlamydodon) between cyanoabacteria
Excellent women in science
A second highlight for Engelmann in 2019 was the WISE-award that was granted to her by NWO, the Dutch Research Council. This award is meant as a stimulus to women who excel in science. Engelmann: ‘To date, there is still a lot of inequality in gender, when it comes to scientists in higher positions. One thing that could make a difference, is if there were more female role models. More female professors and senior scientist can make female students realize that there is a future in science for them too!’ With Engelmann already holding a tenure track position herself, she spent the awarded money on a new post-doc scientist in her group. ‘I am happy this post-doc turned out to be a woman, too’, she adds.
‘By the beginning of 2022, she will board on an expedition to Antarctica, to study the coastal microbial communities there. We hope to analyse and predict how microbial life in that region might respond to climate change, taking the interactions among themselves and the environment into account.’ The WISE grant allows Engelmann to compare the microbial communities in the North and Wadden Sea with microbial communities in coastal waters of Antarctica.
Filtration device inside a lab container on RV Navicula
Plankton bloom of Diatoms and Phaeocystis
‘Microbial communities in Antarctica feed the global food web’, Engelmann says. ‘Therefore, it is crucial to understand how they might respond to, for example, increasing temperatures and lower salinity due to climate change. We are starting to realise that microbial interactions are important, but it will be a long way to truly understanding how microbial communities work. I hope that my findings can one day also be used to refine ocean food web models.’
Steep learning curve
Regarding her own first sea-going experience, Engelmann has proven to have a pretty steep learning curve. In the spring of 2020, just before the outbreak of COVID-19, she joined her second expedition on the RV Navicula, now as a research leader herself. ‘It is good to get an appreciation of the scientific processes in the field. It shows you, for example, what sources of variation between samplings there are, that you wouldn’t think of otherwise. It makes you look at the data on your computer screen with different eyes than before.’
Taking a water sample from the Wadden Sea on board of RV Navicula